Logging and progress¶

Calculation log¶

During a real calculation, gmx_MMPBSA.log is created in the working directory. In an MPI run, rank 0 owns this master log; non-master ranks do not truncate or append to it. A non-master rank creates a rank-specific diagnostic log only if it emits an error.

The log uses a compact format:

[INFO   ] Complex completed: 10 frames in 00:01 (9.99 frame/s)

The file contains DEBUG records as well as normal lifecycle, warning, and error records. Terminal output remains at INFO level so it stays readable. --help, --version, and other command-line parsing actions do not create or replace a previous calculation log. A real calculation or --rewrite-output starts a fresh log, so concurrent runs should use separate working directories.

Monitor a batch job with:

tail -f gmx_MMPBSA.log

The final summary reports warning and error records counted directly by the logging system. Multiline messages count as one record. Fatal exceptions terminate the run; a nonfatal error record does not change the exit status.

Progress display modes¶

Select a mode with --progress-style:

Rich and classic renderers do not write animated bars or ANSI control sequences to the calculation log. Progress checkpoints use MPI-rank terminology and are emitted at bounded percentage milestones. If an external calculation stops producing frames for the default five-minute stall interval, the log emits a rate-limited waiting notice rather than repeating a warning on every poll.

Warnings and errors¶

Warnings are reserved for conditions that may affect interpretation, accuracy, performance, compatibility, or requested behavior. Expected automatic actions—such as assigning QM charges, preparing GBNSR6 topology copies, or assigning missing chain IDs—are informational records. Scientific approximations, fallback paths, incomplete convergence, and user-value mismatches remain warnings.

Fatal input and setup errors are recorded once with a concise message. Unexpected internal exceptions include traceback context in the log. By default, a failed gmx_MMPBSA or amber_MMPBSA calculation creates a diagnostic zip bundle and records its path so the archive can be attached to a bug report. The bundle can contain logs, input and setup files, generated intermediates, and samples of up to five trajectory frames; review its contents before sharing it.

Use --no-error-bundle to disable automatic bundle creation, for example when input coordinates must not be copied into an archive:

gmx_MMPBSA --no-error-bundle -O -i mmpbsa.in ...

The same option is accepted by amber_MMPBSA. It affects only diagnostic bundle creation after a failure; normal logging and the calculation exit status are unchanged.

Message text is intended for people, not as a stable machine-readable interface. Scripts should use result files and exit status rather than parsing logging wording.